Put it through a redirect service, such as the one found at www.remotelyhosted.com, or your own redirect CGI script. This will count the clicks and then redirect to the ad, so you will have two counts to compare.
Hope that helps,
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is there any way i can know the actual click-thru stat of banners which provided by ad company.so that i wont be fooled by those company
What is the ad company serving the ads? Some of us might have some experiences to share.